Skip to main content

Knowledge Base

The knowledge base is a local, searchable corpus of your own reference material — clinical guidelines, journal articles, protocols — that Phlox uses to ground its chat answers. It lives in documents.sqlite as vector embeddings (via sqlite-vec) and stays on your machine.

There is no separate "document chat" screen. You build the knowledge base on the Documents page, and the chat surfaces (the Agent Dashboard and the patient Reference Chat) query it automatically.

Knowledge BaseKnowledge Base

Managing collections​

Open the Documents page and go to the Knowledge Base tab. There you can:

  • Upload a single PDF, or bulk-upload many via drag-and-drop.
  • Each document is auto-classified (by the LLM) into a disease-named collection, with a title, source, and focus area (e.g. guidelines, diagnosis, treatment). You can override these before committing, and edit them later.
  • Rename collections, delete individual documents or whole collections, and download the original PDFs.

When you change your embedding model, re-embed everything from Settings → Model Settings → RAG.

The knowledge base is intended for non-PHI reference material. It is stored in a separate, unencrypted database — keep clinical data out of it. See Security.

Querying the knowledge base​

You don't chat on the Documents page. Instead, the knowledge base is queried automatically from:

  • The Agent Dashboard chat (general medical questions), and
  • The patient Reference Chat (from the Floating Action Menu).

When the model decides a question would benefit, it calls the get_relevant_literature tool, retrieves the most relevant passages from the matching collection, and answers with structured inline citations ([1], [2]…) plus a sources footer. Where the original PDF is stored, a citation links to a downloadable copy.

  • The get_relevant_literature tool is auto-hidden until the knowledge base has at least one collection.
  • External literature tools (PubMed, Wikipedia) ship disabled by default — enable them in Settings → Tools if you want chat to also pull from those external sources.